Changes for page Using JupyterHub in HDC

Last modified by Dennis Segebarth on 2026/02/26 12:16
From version 21.1
edited by Dennis Segebarth
on 2026/02/26 12:16
Change comment: There is no comment for this version
To version 5.1
edited by Susan Evans
on 2023/07/14 17:11
Change comment: There is no comment for this version

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2 2  {{toc depth="2"/}}
3 3  {{/box}}
4 4  
5 -{{warning}}
6 -**Disclaimer:** This article may contain screenshots from other Pilot-based deployments. Differences only apply to variations in branding and color schemes, not the functionalities covered in this article, though.
7 -{{/warning}}
8 8  
9 -
10 10  JupyterHub is an open-source, multi-user version of Jupyter Notebook for performing analysis of Project files in the Core. More information can be found in the application documentation [[https:~~/~~/jupyter.org/>>https://jupyter.org/]].
11 11  
12 -[[image:1723798240534-407.png||height="189" width="291"]]
8 +[[image:Jupyterhub-Logo-300x100px cropped.png||height="13%" width="20%"]]
13 13  
14 14  
15 15  = How it Works =
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29 29  
30 30  JupyterHub is configured at the time of Project Setup. If you launch JupyterHub and receive a notice that it hasn’t been deployed for your project, please contact your Platform Administrator.
31 31  
32 -{{info}}
33 -If you access JupyterHub of the HealthDataCloud Test Project, please be aware that the resources are limited for each user to: 2 GB of persistent storage volume, 4 GB memory, and a single CPU. These limitations can easily be adjusted for new Projects.
34 -{{/info}}
35 -
36 36  = Launching JupyterHub =
37 37  
38 -[[image:1723798257792-201.png||height="121" width="349"]]
30 +[[image:HDC Project Workspace tool navigation Jupyterhub v1.0.0 2023-05-25.png||height="9%" width="25%"]]
39 39  
40 40  1. Launch your Project and click the **JupyterHub icon** in the left menu bar.
41 41  1. Click **Sign in with Keycloak** to initiate your session. JupyterHub automatically authenticates with your existing username and password and launches your session - no additional sign-in is required.
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50 50  1. In the Launcher, click the **Python 3 Notebook **icon, or click **File > New > Notebook**.
51 51  1. Create your Notebook.
52 52  
53 -[[image:1723798278604-114.png||height="376" width="865"]]
45 +[[image:Project Workspace Jupyter Create Python Notebook v2.1.6 2023-02-07.png||height="22%" width="50%"]]
54 54  
55 55  = Launching the Terminal =
56 56  
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59 59  1. In the Launcher, click the **Terminal **icon, or click **File > New > Terminal**.
60 60  1. The terminal window opens.
61 61  
62 -[[image:1723798293872-992.png||height="162" width="863"]]
54 +[[image:Project Workspace Jupyter Launch Terminal v2.1.6 2023-02-07.png||height="9%" width="50%"]]
63 63  
64 64  Ubuntu is used to host Jupyter Notebook. Use the command cat /etc/os-release to determine to current version of Ubuntu:
65 65  
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196 196  
197 197  Afterwards, the environment will be listed when you open the Launcher to open a new Jupyter Notebook:
198 198  
199 -[[image:1723798325144-485.png||height="436" width="867"]]
191 +[[image:Project Workspace Jupyter view new Kernel 2023-07-11.png||height="25%" width="50%"]]
200 200  
201 201  
202 202  and also from each opened Notebook, e.g., via **Kernel > Change Kernel…** :
203 203  
204 -[[image:1723798338447-469.png||height="317" width="247"]]
196 +[[image:Project Workspace Jupyter Kernel change Kernel dropdown 2023-07-11.png||height="32%" width="25%"]]
205 205  
206 206  = Installing New Python Packages =
207 207  
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291 291  * Open the login window and enter your HDC username and password (i.e. your EBRAINS account credentials).
292 292  * Grant access by clicking **Yes**.
293 293  
294 -[[image:1723798355215-434.png||height="352" width="379"]]
286 +[[image:Pilotcli Jupyter user login Grant Access window v2.4.0 2023-05-25.png||height="28%" width="30%"]]
295 295  
296 -[[image:1723798365454-527.png||height="123" width="376"]]
288 +[[image:Pilotcli Jupyter user login Device Login Successful v2.4.0 2023-05-25.png||height="10%" width="30%"]]
297 297  
298 298  * After successful confirmation, return to the terminal in your JupyterHub browser tab.
299 299  
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376 376  
377 377  The file “Chemical Tracking Data.csv” can be viewed in the JupyterHub graphical user interface:
378 378  
379 -[[image:1723798383409-873.png||height="267" width="874"]]
371 +[[image:Jupyter downloaded file in Home folder v2.4.11 2023-05-25 1850.png||height="15%" width="50%"]]
380 380  
381 381  
382 382  == Uploading Project Data from JupyterHub using the Pilot Command Line Interface ==
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417 417  Chemical Tracking Data rev.csv Chemical Tracking Data.csv
418 418  {{/code}}
419 419  
420 -[[image:1723798397694-530.png||height="217" width="863"]]
412 +[[image:Jupyterhub file upload back to core v2.4.11 2023-05-25 1926.png||height="13%" width="50%"]]
421 421  
422 422  ----
423 423  
424 -Copyright © 2023-2026 [[Indoc Systems>>url:https://www.indocsystems.com]].
416 +Copyright © 2023 [[Indoc Systems>>url:https://www.indocsystems.com]].
425 425  
426 426  HealthDataCloud is powered by Pilot technology, a product of [[Indoc Systems>>url:https://www.indocsystems.com]].
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